Extending the models for XX and XO data, so as to keep a consensus network as far as possible.

Steps to find the common link to be added :
1.) Read in the extension.csv for both cell lines
2.) Remove links from TFs and Ligands
3.) Retain only links that have adjusted p-value < 0.005 and value !=0
4.) Calculate %improvement in residual for each cell line
5.) Find the intersection list,(Links that appear in both lists)
6.) Calculate the sum of %improvement in residual
7.) Order the intersection list by descending order of sum of %improvement in residual.
8.) Add the link with Max sum of %improvement to both models.

XX

Initial-Fit

Model residual = 2056

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 2.42131392715506 1279.26842190019 18 777.03304731989 2 0 0
2 171 Gsk3 Akt 2.00319210991692 1288.71936968838 18 767.582099531694 2 0 0
3 183 Gsk3 Pi3k 11.6958612439558 1289.13305769314 18 767.168411526934 2 0 0
4 176 Gsk3 Fgfr 0.191487396968345 1372.05906759666 18 684.242401623412 2 0 0
5 409 Stat3 Igfr 0.996921537359289 1503.1132453024 17 553.188223917678 1 0 0
6 220 Jak Igfr 0.0589008292325789 1503.11324606226 17 553.188223157812 1 0 0
7 407 Stat3 Fgfr 0.30045121609781 1515.31854310863 17 540.982926111448 1 0 0
8 218 Jak Fgfr 0.0177657697244617 1515.31854320347 17 540.982926016607 1 0 0
9 225 Jak Pi3k 0.304239596610088 1519.02257751537 17 537.278891704703 1 0 0
10 414 Stat3 Pi3k 5.16273122626625 1519.02257754846 17 537.278891671613 1 0 0
11 402 Stat3 Akt 0.536041832355594 1523.34265153029 17 532.958817689789 1 0 0
12 213 Jak Akt 0.0316727189204748 1523.3426515508 17 532.958817669279 1 0 0
13 92 Bmp4r Fgfr 0.478856488508333 1854.77455344286 18 201.526915777219 2 0 0
14 8 Activin Fgfr -0.792404679309249 1894.64741083532 17 161.654058384755 1 0 0
15 29 Actr Fgfr -0.792426381232715 1894.64741083582 17 161.654058384257 1 0 0
16 386 Smad2 Fgfr -2.41663924959203 1894.6474108505 17 161.654058369575 1 0 0
17 27 Actr Erk -0.753277609134912 1908.45360146418 17 147.847867755896 1 0 0
18 6 Activin Erk -0.753278420193751 1908.45360152116 17 147.847867698919 1 0 0
19 384 Smad2 Erk -2.29713339325363 1908.4536019225 17 147.847867297581 1 0 0
20 13 Activin Mek -0.179931690911313 1930.52896311401 17 125.772506106068 1 0 0

LA1:Jak -> Fgfr

Model residual = 1515

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 178 Gsk3 Igfr 1.25939585777359 971.27294791213 19 543.729024250194 2 0 0
2 171 Gsk3 Akt 1.6831752588437 980.754734088454 19 534.247238073871 2 0 0
3 183 Gsk3 Pi3k 0.94778669813224 981.104898027555 19 533.897074134769 2 0 0
4 176 Gsk3 Fgfr 0.0366184025654162 1042.99093722463 19 472.011034937691 2 0 0
5 180 Gsk3 Lifr 4.73772797305236 1186.00515901316 19 328.996813149167 2 0 0
6 179 Gsk3 Jak 4.19330704676957 1186.00515913941 19 328.99681302291 2 0 0
7 92 Bmp4r Fgfr 0.142967791901535 1379.29321392992 19 135.708758232408 2 0 0
8 95 Bmp4r Jak 1.00624151625726 1405.40002955066 19 109.601942611666 2 0 0
9 96 Bmp4r Lifr 1497.36619598657 1405.40002957818 19 109.601942584148 2 0 0
10 90 Bmp4r Erk 10.0000035470859 1409.88137320897 19 105.120598953353 2 0 0
11 6 Activin Erk -0.615067221342907 1431.05413340261 18 83.9478387597117 1 0 0
12 27 Actr Erk -0.615064037570902 1431.05413341887 18 83.9478387434553 1 0 0
13 384 Smad2 Erk -1.87565984065468 1431.05413348062 18 83.947838681702 1 0 0
14 97 Bmp4r Mek 0.0949137691618458 1432.5284556259 19 82.4735165364261 2 0 0
15 100 Bmp4r Raf 0.0949137691618458 1432.5284556259 19 82.4735165364261 2 0 0
16 101 Bmp4r Ras 0.0949137691618458 1432.5284556259 19 82.4735165364261 2 0 0
17 409 Stat3 Igfr 41.6000915195664 1435.74300198135 18 79.258970180972 1 0 0
18 220 Jak Igfr 0.345374963521373 1435.74303252704 18 79.2589396352821 1 0 0
19 29 Actr Fgfr -0.183065321096944 1436.60116939315 18 78.40080276917 1 0 0
20 8 Activin Fgfr -0.183046931072957 1436.60116944695 18 78.4008027153752 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 99.999999999854 842.133054008928 21 128.960291421982 2 0 0
2 90 Bmp4r Erk 9.99999499632267 866.494171747015 21 104.599173683895 2 0 0
3 96 Bmp4r Lifr 25.7064031039016 881.448217175917 21 89.6451282549929 2 0 0
4 95 Bmp4r Jak 100.000000001115 886.771476140527 21 84.321869290383 2 0 0
5 97 Bmp4r Mek 100 890.81900039849 21 80.2743450324205 2 0 0
6 100 Bmp4r Raf 100 890.81900039849 21 80.2743450324205 2 0 0
7 101 Bmp4r Ras 100 890.81900039849 21 80.2743450324205 2 0 0
8 27 Actr Erk -0.394642320565512 894.001119838159 20 77.0922255927509 1 0 0
9 384 Smad2 Erk -1.00078877548469 899.540237807531 20 71.5531076233797 1 0 0
10 6 Activin Erk -0.998845367517194 899.586763671751 20 71.5065817591588 1 0 0
11 402 Stat3 Akt 0.000966866604946071 900.694714212654 20 70.3986312182562 1 0 0
12 213 Jak Akt 0.000868717817083809 902.501584876284 20 68.5917605546265 1 1.11022302462516e-16 3.7858605139718e-14
13 414 Stat3 Pi3k 0.000534395891113235 902.521570755887 20 68.5717746750234 1 1.11022302462516e-16 3.7858605139718e-14
14 219 Jak Gsk3 4.91337327431707e-05 902.655364118355 20 68.4379813125548 1 1.11022302462516e-16 3.7858605139718e-14
15 408 Stat3 Gsk3 0.00019806551800519 902.719647470625 20 68.3736979602849 1 1.11022302462516e-16 3.7858605139718e-14
16 220 Jak Igfr 4.58765783114058e-05 902.823729778531 20 68.2696156523795 1 1.11022302462516e-16 3.7858605139718e-14
17 225 Jak Pi3k 0.000144282736715549 903.06809561287 20 68.0252498180402 1 1.11022302462516e-16 3.7858605139718e-14
18 13 Activin Mek -0.142309590647939 903.825617653137 20 67.2677277777732 1 2.22044604925031e-16 7.57172102794356e-14
19 16 Activin Raf -0.142309590647939 903.825617653137 20 67.2677277777732 1 2.22044604925031e-16 7.57172102794356e-14
20 17 Activin Ras -0.142309590647939 903.825617653137 20 67.2677277777732 1 2.22044604925031e-16 7.57172102794356e-14

LA3:Erk->Raf

Model residual = 932

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 99.999999999802 801.088727048395 22 131.218358963433 2 0 0
2 90 Bmp4r Erk 9.99998514905258 824.661884478448 22 107.645201533381 2 0 0
3 95 Bmp4r Jak 10.000365033373 839.926929288777 22 92.380156723051 2 0 0
4 96 Bmp4r Lifr 24.5394306134207 840.772728814415 22 91.5343571974136 2 0 0
5 27 Actr Erk -0.795025862753663 845.87550610572 21 86.4315799061079 1 0 0
6 6 Activin Erk -0.99907385599084 848.788099982257 21 83.5189860295712 1 0 0
7 97 Bmp4r Mek 99.9999999999317 849.797583505277 22 82.5095025065517 2 0 0
8 100 Bmp4r Raf 99.9999999999317 849.797583505277 22 82.5095025065517 2 0 0
9 101 Bmp4r Ras 99.9999999999317 849.797583505277 22 82.5095025065517 2 0 0
10 34 Actr Mek -0.180491377462496 863.452853253678 21 68.85423275815 1 1.11022302462516e-16 3.77475828372554e-14
11 38 Actr Ras -0.180491377462496 863.452853253678 21 68.85423275815 1 1.11022302462516e-16 3.77475828372554e-14
12 37 Actr Raf -0.180490869013328 863.452876137015 21 68.8542098748131 1 1.11022302462516e-16 3.77475828372554e-14
13 13 Activin Mek -0.206137831316083 863.863425358187 21 68.4436606536414 1 1.11022302462516e-16 3.77475828372554e-14
14 16 Activin Raf -0.206137831316083 863.863425358187 21 68.4436606536414 1 1.11022302462516e-16 3.77475828372554e-14
15 17 Activin Ras -0.20613783142176 863.863425379486 21 68.4436606323425 1 1.11022302462516e-16 3.77475828372554e-14
16 402 Stat3 Akt 0.000635183887555201 865.364267496751 21 66.9428185150776 1 3.33066907387547e-16 1.13242748511766e-13
17 414 Stat3 Pi3k 0.000518857758045781 865.366206617083 21 66.9408793947449 1 3.33066907387547e-16 1.13242748511766e-13
18 213 Jak Akt 0.00017416985715661 865.492634959915 21 66.8144510519138 1 3.33066907387547e-16 1.13242748511766e-13
19 219 Jak Gsk3 6.00803035324522e-05 865.619488022754 21 66.6875979890743 1 3.33066907387547e-16 1.13242748511766e-13
20 408 Stat3 Gsk3 0.000236749876313866 865.716938979118 21 66.5901470327104 1 3.33066907387547e-16 1.13242748511766e-13

LA4:Bmp4r->Fgfr

Model residual = 798

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 213 Jak Akt 0.000590489017567981 739.229086661648 23 59.0993438091966 1 1.49880108324396e-14 5.08093567219702e-12
2 402 Stat3 Akt 0.00143785270965888 739.237261105938 23 59.0911693649061 1 1.50990331349021e-14 5.11857223273181e-12
3 408 Stat3 Gsk3 0.000161535158831082 739.389103869765 23 58.9393266010788 1 1.62092561595273e-14 5.49493783807976e-12
4 414 Stat3 Pi3k 0.00121345027223676 739.438794827005 23 58.8896356438395 1 1.66533453693773e-14 5.6454840802189e-12
5 409 Stat3 Igfr 0.000238645943751433 739.459695604236 23 58.8687348666083 1 1.68753899743024e-14 5.72075720128851e-12
6 225 Jak Pi3k 0.000339572303764401 739.482184841936 23 58.8462456289077 1 1.70974345792274e-14 5.79603032235809e-12
7 219 Jak Gsk3 5.75384756385806e-06 741.319780049039 23 57.0086504218051 1 4.34097202628436e-14 1.4715895169104e-11
8 166 Fgfr Smad2 0.613940596124831 751.428147627999 23 46.9002828428449 1 7.46924744277067e-12 2.53207488309926e-09
9 149 Fgfr Actr 0.621893954429388 751.508305274885 23 46.8201251959592 1 7.78099806808541e-12 2.63775834508095e-09
10 220 Jak Igfr 9.33133591113448e-06 752.573730447935 23 45.7547000229091 1 1.34027233755774e-11 4.54352322432074e-09
11 412 Stat3 Mek -0.322700346014772 760.638897404767 23 37.6895330660772 1 8.29484481101872e-10 2.81195239093535e-07
12 415 Stat3 Raf -0.322700345153605 760.638903944857 23 37.6895265259869 1 8.29487256659434e-10 2.81196180007548e-07
13 416 Stat3 Ras -0.322700343573217 760.638911816593 23 37.6895186542509 1 8.29490587328507e-10 2.81197309104364e-07
14 6 Activin Erk -1 760.672445555343 23 37.6559849155016 1 8.43873637634829e-10 2.86073163158207e-07
15 27 Actr Erk -0.327920237445887 761.50178986529 23 36.8266406055541 1 1.29113841840223e-09 4.37695923838356e-07
16 384 Smad2 Erk -1 761.50178986529 23 36.8266406055541 1 1.29113841840223e-09 4.37695923838356e-07
17 86 Bmp4r Actr 0.1 763.095768421458 23 35.2326620493858 1 2.92575230709247e-09 9.91830032104347e-07
18 103 Bmp4r Smad2 0.1 763.095768421458 23 35.2326620493858 1 2.92575230709247e-09 9.91830032104347e-07
19 34 Actr Mek -0.146633988480433 763.138120060493 23 35.1903104103511 1 2.99007585358169e-09 1.01363571436419e-06
20 37 Actr Raf -0.146633988480433 763.138120060493 23 35.1903104103511 1 2.99007585358169e-09 1.01363571436419e-06

LA5:Bmp4r->Smad2

Model residual = 752

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 213 Jak Akt 0.000672293573133048 691.925584708851 24 60.3660089699949 1 7.88258347483861e-15 2.66431321449545e-12
2 402 Stat3 Akt 0.00211744007746199 691.936496458501 24 60.355097220345 1 7.88258347483861e-15 2.66431321449545e-12
3 408 Stat3 Gsk3 0.000104743258542005 693.264637751086 24 59.0269559277596 1 1.55431223447522e-14 5.25357535252624e-12
4 219 Jak Gsk3 0.000135691917358666 693.27911176721 24 59.0124819116364 1 1.56541446472147e-14 5.29110089075857e-12
5 220 Jak Igfr 8.45842269446776e-05 693.289403198911 24 59.0021904799352 1 1.57651669496772e-14 5.32862642899089e-12
6 414 Stat3 Pi3k 0.000369542279233321 693.315794571635 24 58.9757991072107 1 1.59872115546023e-14 5.40367750545558e-12
7 409 Stat3 Igfr 0.0002083723529172 693.319030345566 24 58.9725633332802 1 1.59872115546023e-14 5.40367750545558e-12
8 225 Jak Pi3k 7.84048006625031e-05 693.322399334032 24 58.969194344814 1 1.59872115546023e-14 5.40367750545558e-12
9 415 Stat3 Raf -0.262229144239828 710.168650740647 24 42.1229429381988 1 8.57116599917163e-11 2.89705410772001e-08
10 412 Stat3 Mek -0.261705296064354 710.265460647682 24 42.0261330311636 1 9.00617358468025e-11 3.04408667162192e-08
11 416 Stat3 Ras -0.262177220108215 710.283256385081 24 42.0083372937648 1 9.08850772418646e-11 3.07191561077502e-08
12 27 Actr Erk -0.371619820349514 713.22675650787 24 39.0648371709758 1 4.099616202069e-10 1.38567027629932e-07
13 6 Activin Erk -1 714.825242712482 24 37.4663509663636 1 9.30037380442172e-10 3.14352634589454e-07
14 34 Actr Mek -0.136052413177117 720.396811300815 24 31.894782378031 1 1.62753746035804e-08 5.50107661601018e-06
15 37 Actr Raf -0.136052413177117 720.396811300815 24 31.894782378031 1 1.62753746035804e-08 5.50107661601018e-06
16 38 Actr Ras -0.136052413177117 720.396811300815 24 31.894782378031 1 1.62753746035804e-08 5.50107661601018e-06
17 13 Activin Mek -0.1 721.188477632188 24 31.1031160466578 1 2.44678290961531e-08 8.27012623449975e-06
18 16 Activin Raf -0.1 721.188477632188 24 31.1031160466578 1 2.44678290961531e-08 8.27012623449975e-06
19 17 Activin Ras -0.1 721.188477632188 24 31.1031160466578 1 2.44678290961531e-08 8.27012623449975e-06
20 194 Igfr Bmp4r 29.3494749172637 721.822478200611 24 30.4691154782354 1 3.39224202061672e-08 1.14657780296845e-05

LA6:Jak->Gsk3

Model residual = 692

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 395 Smad2 Ras -0.520227054632169 634.791793501334 25 57.0961836376457 1 4.15223411209809e-14 1.39930289577706e-11
2 391 Smad2 Mek -0.520224492027596 634.79206932469 25 57.0959078142902 1 4.15223411209809e-14 1.39930289577706e-11
3 394 Smad2 Raf -0.520315526062302 634.796188345837 25 57.0917887931425 1 4.16333634234434e-14 1.40304434737004e-11
4 6 Activin Erk -0.999345548724999 637.427357738515 25 54.4606194004654 1 1.58539847916472e-13 5.34279287478511e-11
5 27 Actr Erk -0.37179748102256 644.643958629874 25 47.2440185091064 1 6.26765306321886e-12 2.11219908230476e-09
6 17 Activin Ras -0.168376765358166 645.235768679448 25 46.6522084595322 1 8.47710790452538e-12 2.85678536382505e-09
7 16 Activin Raf -0.168376762341466 645.235898675256 25 46.6520784637239 1 8.4776630160377e-12 2.8569724364047e-09
8 13 Activin Mek -0.168376750025262 645.235931473473 25 46.6520456655073 1 8.47788506064262e-12 2.85704726543656e-09
9 38 Actr Ras -0.169830198649673 645.423261607989 25 46.4647155309913 1 9.32831589750549e-12 3.14364245745935e-09
10 34 Actr Mek -0.169830203481362 645.423261762603 25 46.4647153763764 1 9.32831589750549e-12 3.14364245745935e-09
11 37 Actr Raf -0.169830204271531 645.423261787517 25 46.4647153514626 1 9.32831589750549e-12 3.14364245745935e-09
12 8 Activin Fgfr -0.288647326059392 651.91144488931 25 39.97653224967 1 2.57032395367673e-10 8.66199172389058e-08
13 29 Actr Fgfr -1.1227849623485 652.398389756473 25 39.4895873825069 1 3.29813398813883e-10 1.11147115400279e-07
14 384 Smad2 Erk -1 657.743023645154 25 34.1449534938259 1 5.11557340932001e-09 1.72394823894084e-06
15 194 Igfr Bmp4r 8.69062159066789 660.382844095936 25 31.5051330430441 1 1.98913735482975e-08 6.70339288577626e-06
16 5 Activin Bmp4r -0.999734483557364 660.499041300084 25 31.3889358388959 1 2.11180902764951e-08 7.11679642317885e-06
17 173 Gsk3 Bmp4r 6.92421551621703 662.907037605092 25 28.9809395338883 1 7.30939759829852e-08 2.4632669906266e-05
18 47 Akt Bmp4r 0.64596238791056 665.902502330797 25 25.9854748081824 1 3.43995790186291e-07 0.00011592658129278
19 53 Akt Jak 0.406595903108491 667.591135952838 25 24.2968411861416 1 8.25743662224987e-07 0.000278275614169821
20 54 Akt Lifr 0.511576373594528 667.625558503126 25 24.2624186358538 1 8.40633270104973e-07 0.000283293412025376

LA7:Actr-> Ras

Model residual = 645

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 117 Erk Lifr 0.268755400333778 622.783428655144 26 22.2876353916071 1 2.34713069224846e-06 0.000788635912595483
2 116 Erk Jak 0.18084790833206 622.792146331337 26 22.2789177154143 1 2.35781065238694e-06 0.000792224379202012
3 263 Mek Jak 0.628804792747773 622.812892231892 26 22.2581718148589 1 2.38342277170123e-06 0.000800830051291613
4 264 Mek Lifr 0.887686683722006 623.178368385604 26 21.8926956611473 1 2.88329326203485e-06 0.00096878653604371
5 129 Fgf4 Akt -6.14256398055869e-05 623.586609795386 26 21.4844542513646 1 3.56708741899858e-06 0.00119854137278352
6 404 Stat3 Bmp4r 1.00089570921509 623.594371140224 26 21.476692906527 1 3.58155437374386e-06 0.00120340226957794
7 282 NoLif Gsk3 0.00222377149193153 623.643646097885 26 21.4274179488654 1 3.67478515017616e-06 0.00123472781045919
8 141 Fgf4 Pi3k -6.70777006023923e-06 623.710069181024 26 21.3609948657264 1 3.80432699209621e-06 0.00127825386934433
9 135 Fgf4 Gsk3 -1.8958614224253e-05 623.748585000097 26 21.3224790466535 1 3.88153145558512e-06 0.0013041945690766
10 136 Fgf4 Igfr -2.0859693155469e-05 623.749787633864 26 21.3212764128864 1 3.88396726791473e-06 0.00130501300201935
11 240 Lifr Gsk3 0.00214290819341989 625.290101946306 26 19.7809621004445 1 8.68433817491354e-06 0.00291793762677095
12 53 Akt Jak 0.339733855550895 625.319455669243 26 19.7516083775083 1 8.81874482161482e-06 0.00296309826006258
13 54 Akt Lifr 0.430509302565306 625.365294819223 26 19.7057692275279 1 9.03282561814933e-06 0.00303502940769817
14 234 Lifr Akt 0.00258906312267188 625.987566745774 26 19.0834973009772 1 1.25122153257218e-05 0.00420410434944252
15 276 NoLif Akt 0.00414955266786068 626.002229008816 26 19.0688350379351 1 1.26087158681676e-05 0.00423652853170431
16 283 NoLif Igfr 0.000604783635341718 626.214884924157 26 18.856179122594 1 1.40953750081829e-05 0.00473604600274945
17 241 Lifr Igfr 0.000554957195045443 626.219674493104 26 18.8513895536469 1 1.41308122647565e-05 0.00474795292095818
18 110 Erk Bmp4r 0.524444690360049 626.288444459756 26 18.7826195869944 1 1.46496085514647e-05 0.00492226847329214
19 314 Pi3k Stat3 0.237625830445455 626.767064558488 26 18.3039994882631 1 1.88311404523134e-05 0.0063272631919773
20 62 Akt Stat3 0.0898175512556101 626.848242709912 26 18.2228213368384 1 1.96510056411636e-05 0.00660273789543097

LA8:Lifr->Akt

Model residual = 622

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 263 Mek Jak 0.172729443226609 597.615701568062 27 24.446293304433 1 7.64103798567284e-07 0.00025597477252004
2 116 Erk Jak 0.0534848707956389 597.638422959988 27 24.423571912507 1 7.73168714274242e-07 0.000259011519281871
3 324 Raf Gsk3 -0.0179987496186676 600.063417054375 27 21.9985778181202 1 2.72852570126769e-06 0.000914056109924676
4 318 Raf Akt -0.005245130375493 600.327486939411 27 21.7345079330842 1 3.13108111216209e-06 0.0010489121725743
5 215 Jak Bmp4r 0.639517526466721 600.390823443118 27 21.6711714293771 1 3.23618385467128e-06 0.00108412159131488
6 404 Stat3 Bmp4r 0.549243104303257 600.405542038324 27 21.6564528341711 1 3.26111102788573e-06 0.00109247219434172
7 325 Raf Igfr -0.000531215229730128 600.425971758063 27 21.6360231144319 1 3.29603008286661e-06 0.00110417007776031
8 110 Erk Bmp4r 0.224998720461391 600.858414417527 27 21.2035804549686 1 4.12992273801649e-06 0.00138352411723552
9 257 Mek Bmp4r 0.741743718962159 601.13844721491 27 20.9235476575856 1 4.77982640612051e-06 0.00160124184605037
10 323 Raf Fgfr -0.51934741482032 601.399694231024 27 20.662300641471 1 5.47840947329181e-06 0.00183526717355276
11 403 Stat3 Bmp4 1 602.19057884556 27 19.8714160269353 1 8.28295732890894e-06 0.0027747907051845
12 214 Jak Bmp4 1 602.359191764471 27 19.7028031080241 1 9.04685656644144e-06 0.00303069694975788
13 250 Lifr Smad2 -0.212758988433461 602.971158541703 27 19.0908363307919 1 1.24641919545532e-05 0.00417550430477532
14 292 NoLif Smad2 -0.212728418167504 602.971201442927 27 19.0907934295682 1 1.24644721427591e-05 0.0041755981678243
15 179 Gsk3 Jak 0.159380197524893 602.973363565298 27 19.0886313071977 1 1.24786011710398e-05 0.00418033139229833
16 180 Gsk3 Lifr -0.218139745475387 602.975115333522 27 19.0868795389734 1 1.24900604124845e-05 0.00418417023818231
17 306 Pi3k Lifr 1 602.977000836813 27 19.0849940356819 1 1.25024062945789e-05 0.00418830610868393
18 305 Pi3k Jak 0.220084281136024 602.980671699653 27 19.081323172842 1 1.25264775044931e-05 0.00419636996400519
19 53 Akt Jak 0.074103669616181 602.982993948616 27 19.0790009238791 1 1.25417293815877e-05 0.00420147934283188
20 54 Akt Lifr -0.100826844783338 602.985318367688 27 19.076676504807 1 1.25570141863429e-05 0.00420659975242487

LA9: Gsk3->Lifr

Model residual = 603

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 404 Stat3 Bmp4r 0.703029464241858 577.388164176362 28 25.58352110482 1 4.23641940860975e-07 0.000141496408247566
2 215 Jak Bmp4r 0.781592715142783 577.671380957362 28 25.3003043238202 1 4.90631331340197e-07 0.000163870864667626
3 233 Lifr Actr 1 580.057760829538 28 22.9139244516441 1 1.69420106188589e-06 0.000565863154669887
4 250 Lifr Smad2 -0.215960669095827 580.266208036426 28 22.7054772447564 1 1.88828860270274e-06 0.000630688393302715
5 324 Raf Gsk3 -0.0127599822273653 580.833003793259 28 22.1386814879231 1 2.53646998271684e-06 0.000847180974227425
6 318 Raf Akt -0.00549201778173127 581.023780815341 28 21.9479044658412 1 2.80152634635211e-06 0.000935709799681605
7 325 Raf Igfr -0.000358603555390685 581.114590594595 28 21.8570946865874 1 2.93728559874751e-06 0.000981053389981668
8 403 Stat3 Bmp4 1 581.252351369322 28 21.7193339118601 1 3.15594516231421e-06 0.00105408568421295
9 257 Mek Bmp4r 0.741573487356509 581.536451374656 28 21.4352339065262 1 3.65983606032128e-06 0.00122238524414731
10 110 Erk Bmp4r 0.237371126911125 581.572333086904 28 21.3993521942782 1 3.72897158251728e-06 0.00124547650856077
11 214 Jak Bmp4 1 582.375346340634 28 20.5963389405488 1 5.67044488131163e-06 0.00189392859035808
12 323 Raf Fgfr -0.651758962552214 582.964355275338 28 20.0073300058446 1 7.71458728021646e-06 0.0025766721515923
13 275 NoLif Actr 1 583.781949274832 28 19.1897360063508 1 1.18348022700721e-05 0.00395282395820408
14 292 NoLif Smad2 -0.197590131842584 583.991190890854 28 18.9804943903284 1 1.3206160955348e-05 0.00441085775908623
15 109 Erk Bmp4 1 584.007825088223 28 18.9638601929597 1 1.3321798475352e-05 0.00444948069076757
16 136 Fgf4 Igfr -0.00474620898869111 584.484210403046 28 18.4874748781361 1 1.71024553248245e-05 0.00571222007849138
17 141 Fgf4 Pi3k -0.00082512342600362 584.578071465324 28 18.3936138158581 1 1.79659106340768e-05 0.00600061415178165
18 418 Stat3 Smad2 0.137631818614857 584.589907416537 28 18.3817778646458 1 1.80778577387741e-05 0.00603800448475055
19 129 Fgf4 Akt -0.00186688134473684 584.6430588496 28 18.3286264315826 1 1.85892783669539e-05 0.0062088189745626
20 229 Jak Smad2 0.228519645206925 584.668860168928 28 18.3028251122541 1 1.88427526850443e-05 0.0062934793968048

LA10:Jak->Bmp4r

Model residual = 572

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 324 Raf Gsk3 -0.0129077660805646 550.743561782836 29 21.494893696155 1 3.54772098398737e-06 0.00118139108766779
2 318 Raf Akt -0.0082648983168449 550.889556186817 29 21.3488992921743 1 3.82840497892278e-06 0.00127485885798129
3 330 Raf Pi3k 1 550.898348573534 29 21.3401069054577 1 3.84600342206998e-06 0.0012807191395493
4 325 Raf Igfr -0.00039132112694365 550.988615095317 29 21.249840383674 1 4.03143940619355e-06 0.00134246932226245
5 323 Raf Fgfr -0.935217355942616 552.373181834613 29 19.8652736443785 1 8.30961425135612e-06 0.00276710154570159
6 136 Fgf4 Igfr -0.00530420000645634 554.567672738664 29 17.6707827403272 1 2.62629850733553e-05 0.00874557402942732
7 141 Fgf4 Pi3k -0.00239829090462578 554.627713585273 29 17.6107418937182 1 2.71052983531472e-05 0.00902606435159802
8 129 Fgf4 Akt -0.00473316854320603 554.650567091834 29 17.5878883871574 1 2.74329972328458e-05 0.00913518807853765
9 135 Fgf4 Gsk3 -0.000140560151348979 554.883068774597 29 17.3553867043946 1 3.10018315397009e-05 0.0103236099027204
10 113 Erk Fgfr 0.0808924489780835 555.747480460477 29 16.4909750185142 1 4.88822006322609e-05 0.0162777728105429
11 260 Mek Fgfr 0.27304145111923 555.77053556514 29 16.4679199138515 1 4.9480256855805e-05 0.0164769255329831
12 262 Mek Igfr 0.00238192736202858 555.867754709726 29 16.3707007692655 1 5.20841604884081e-05 0.0173440254426399
13 115 Erk Igfr 0.000637086366913993 555.873615871624 29 16.3648396073676 1 5.22454785755189e-05 0.0173977443656478
14 255 Mek Akt 0.000104485743978271 555.933650714788 29 16.3048047642036 1 5.39270416263227e-05 0.0179577048615655
15 267 Mek Pi3k 0.000211347500594851 556.008712899796 29 16.2297425791954 1 5.61063023789554e-05 0.0186833986921921
16 120 Erk Pi3k 0.000168519770979185 556.012166519623 29 16.2262889593682 1 5.62086748284729e-05 0.0187174887178815
17 108 Erk Akt 9.10019240854155e-05 556.03076150065 29 16.2076939783415 1 5.67631057993845e-05 0.018902114231195
18 261 Mek Gsk3 0.000304961271424265 556.045910396416 29 16.1925450825752 1 5.72188507366178e-05 0.0190538772952937
19 114 Erk Gsk3 2.60611600775316e-05 556.047339328672 29 16.191116150319 1 5.72620287240255e-05 0.0190682555651005
20 110 Erk Bmp4r 1.15783248669099 556.414950102867 29 15.8235053761244 1 6.95333244429275e-05 0.0231545970394949

XO

Initial-Fit

Model residual = 1604

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 218 Jak Fgfr 11.981597803888 1087.34331543348 17 516.380135548736 1 0 0
2 407 Stat3 Fgfr 16.8350503938008 1087.34331590508 17 516.380135077134 1 0 0
3 405 Stat3 Erk 0.814941963280207 1259.70107135275 17 344.022379629471 1 0 0
4 216 Jak Erk 0.694604529531016 1259.70107135601 17 344.022379626204 1 0 0
5 412 Stat3 Mek 0.16923081767877 1274.91766675172 17 328.8057842305 1 0 0
6 415 Stat3 Raf 0.16923081767877 1274.91766675172 17 328.8057842305 1 0 0
7 416 Stat3 Ras 0.16923081767877 1274.91766675172 17 328.8057842305 1 0 0
8 223 Jak Mek 0.15351255616843 1274.91766677103 17 328.80578421119 1 0 0
9 226 Jak Raf 0.15351255616843 1274.91766677103 17 328.80578421119 1 0 0
10 227 Jak Ras 0.15351255616843 1274.91766677103 17 328.80578421119 1 0 0
11 281 NoLif Fgfr -18.009979214919 1284.20827351376 17 319.515177468463 1 0 0
12 239 Lifr Fgfr -18.7422726078718 1284.20827351794 17 319.515177464278 1 0 0
13 279 NoLif Erk -1.09664062995169 1307.81404092965 17 295.909410052571 1 0 0
14 237 Lifr Erk -1.09664019334166 1307.81404093801 17 295.909410044208 1 0 0
15 286 NoLif Mek -0.23987172214812 1311.08678096065 17 292.636670021565 1 0 0
16 289 NoLif Raf -0.23987172214812 1311.08678096065 17 292.636670021565 1 0 0
17 290 NoLif Ras -0.23987172214812 1311.08678096065 17 292.636670021565 1 0 0
18 244 Lifr Mek -0.239871726502607 1311.08678096201 17 292.636670020209 1 0 0
19 247 Lifr Raf -0.239871726502607 1311.08678096201 17 292.636670020209 1 0 0
20 248 Lifr Ras -0.239871726502607 1311.08678096201 17 292.636670020209 1 0 0

LA1:Jak -> Fgfr

Model residual = 1064

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 118 Erk Mek -1.31339025972559 815.631614413539 18 247.924428476035 1 0 0
2 121 Erk Raf -1.31339025972559 815.631614413539 18 247.924428476035 1 0 0
3 122 Erk Ras -1.31339025972559 815.631614413539 18 247.924428476035 1 0 0
4 269 Mek Ras -5.83501952054796 815.631614580348 18 247.924428309226 1 0 0
5 268 Mek Raf -5.83501188666022 815.631614581427 18 247.924428308147 1 0 0
6 92 Bmp4r Fgfr 9.99999923986765 953.75112020629 19 109.804922683284 2 0 0
7 29 Actr Fgfr -0.10764836408698 960.885942413727 18 102.670100475847 1 0 0
8 8 Activin Fgfr -0.107647596799351 960.885942640167 18 102.670100249407 1 0 0
9 386 Smad2 Fgfr -0.138085925748002 960.885942669891 18 102.670100219683 1 0 0
10 97 Bmp4r Mek 0.0981211494970267 962.159239438493 19 101.396803451081 2 0 0
11 100 Bmp4r Raf 0.0981211494970267 962.159239438493 19 101.396803451081 2 0 0
12 101 Bmp4r Ras 0.0981211494970267 962.159239438493 19 101.396803451081 2 0 0
13 180 Gsk3 Lifr 0.109860277821195 962.880760585377 19 100.675282304197 2 0 0
14 179 Gsk3 Jak 0.109858631677213 962.880760588534 19 100.67528230104 2 0 0
15 90 Bmp4r Erk 99.9999999979996 964.022336777106 19 99.5337061124676 2 0 0
16 6 Activin Erk -0.763290516738629 964.487926098829 18 99.0681167907445 1 0 0
17 384 Smad2 Erk -0.979127651759686 964.487926296968 18 99.0681165926064 1 0 0
18 27 Actr Erk -0.763290245789731 964.487926348719 18 99.0681165408554 1 0 0
19 13 Activin Mek -0.150168575987821 966.972717465691 18 96.5833254238829 1 0 0
20 16 Activin Raf -0.150168575987821 966.972717465691 18 96.5833254238829 1 0 0

LA2:Gsk3->Igfr

Model residual = 971

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 118 Erk Mek -1.31102539748347 720.220047183134 20 250.411228934431 1 0 0
2 121 Erk Raf -1.31102532880172 720.220065387904 20 250.41121072966 1 0 0
3 122 Erk Ras -1.31102532880172 720.220065387904 20 250.41121072966 1 0 0
4 268 Mek Raf -5.6846568341329 720.261786699052 20 250.369489418513 1 0 0
5 269 Mek Ras -5.68545907329192 720.323101198929 20 250.308174918636 1 0 0
6 92 Bmp4r Fgfr 99.9999999999801 867.429100202621 21 103.202175914943 2 0 0
7 97 Bmp4r Mek 0.400693241447973 869.556398196722 21 101.074877920842 2 0 0
8 100 Bmp4r Raf 0.400693241447973 869.556398196722 21 101.074877920842 2 0 0
9 101 Bmp4r Ras 0.400693241447973 869.556398196722 21 101.074877920842 2 0 0
10 90 Bmp4r Erk 10.0000108997077 871.61916843156 21 99.0121076860048 2 0 0
11 384 Smad2 Erk -0.97320275247995 872.347662255345 20 98.2836138622193 1 0 0
12 27 Actr Erk -0.758632117573288 872.351218049663 20 98.280058067901 1 0 0
13 6 Activin Erk -0.758750743424516 872.362833622831 20 98.2684424947339 1 0 0
14 34 Actr Mek -0.151353786235585 875.391707289387 20 95.2395688281772 1 0 0
15 37 Actr Raf -0.151353786235585 875.391707289387 20 95.2395688281772 1 0 0
16 38 Actr Ras -0.151353786235585 875.391707289387 20 95.2395688281772 1 0 0
17 13 Activin Mek -0.15154895490236 875.394010530072 20 95.2372655874927 1 0 0
18 16 Activin Raf -0.15154895490236 875.394010530072 20 95.2372655874927 1 0 0
19 17 Activin Ras -0.15154895490236 875.394010530072 20 95.2372655874927 1 0 0
20 391 Smad2 Mek -0.205821915166234 875.750420043984 20 94.88085607358 1 0 0

LA3:Erk-> Raf

Model residual = 720

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 92 Bmp4r Fgfr 1.00023686459606 611.604908206751 22 108.455870592593 2 0 0
2 97 Bmp4r Mek 10.000045548404 614.927650492786 22 105.133128306557 2 0 0
3 100 Bmp4r Raf 10.000045548404 614.927650492786 22 105.133128306557 2 0 0
4 101 Bmp4r Ras 10.000045548404 614.927650492786 22 105.133128306557 2 0 0
5 13 Activin Mek -1.04944316278497 628.173698552986 21 91.8870802463574 1 0 0
6 16 Activin Raf -1.04944316278497 628.173698552986 21 91.8870802463574 1 0 0
7 17 Activin Ras -1.04743702323325 628.175125659799 21 91.8856531395443 1 0 0
8 395 Smad2 Ras -1.3409222135155 628.186674824743 21 91.8741039746006 1 0 0
9 394 Smad2 Raf -1.34092040010192 628.187259149413 21 91.8735196499308 1 0 0
10 391 Smad2 Mek -1.34091953948239 628.187474739697 21 91.8733040596464 1 0 0
11 34 Actr Mek -1.04471474853502 628.213431685341 21 91.8473471140031 1 0 0
12 38 Actr Ras -1.04471474853502 628.213431685341 21 91.8473471140031 1 0 0
13 37 Actr Raf -1.0447147481121 628.213431729881 21 91.8473470694624 1 0 0
14 8 Activin Fgfr -0.0952693973074134 628.981024973208 21 91.079753826136 1 0 0
15 29 Actr Fgfr -0.0952693973074134 628.981024973208 21 91.079753826136 1 0 0
16 386 Smad2 Fgfr -0.122301329284573 628.981607123193 21 91.0791716761503 1 0 0
17 96 Bmp4r Lifr 139.808109260774 637.060640003752 22 83.0001387955913 2 0 0
18 95 Bmp4r Jak 100.00000000036 637.128120918996 22 82.9326578803481 2 0 0
19 86 Bmp4r Actr 1.00028731719295 638.793468451171 22 81.2673103481731 2 0 0
20 103 Bmp4r Smad2 1.00028731719318 638.793468451186 22 81.2673103481578 2 0 0

LA4:Bmp4r->Fgfr

Model residual = 611

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 103 Bmp4r Smad2 0.174384035193785 530.139590652689 23 81.3413318736128 1 0 0
2 86 Bmp4r Actr 0.174384035158899 530.139590664927 23 81.3413318613752 1 0 0
3 359 Smad1 Actr 1 530.140836811315 23 81.3400857149867 1 0 0
4 376 Smad1 Smad2 1 530.140836811946 23 81.3400857143562 1 0 0
5 355 Ras Smad2 0.985576021132984 545.401350685297 23 66.0795718410048 1 4.44089209850063e-16 1.50546242139171e-13
6 338 Ras Actr 0.985570114502944 545.401766747299 23 66.0791557790027 1 4.44089209850063e-16 1.50546242139171e-13
7 149 Fgfr Actr 0.973897903664458 545.458306481829 23 66.0226160444732 1 4.44089209850063e-16 1.50546242139171e-13
8 166 Fgfr Smad2 0.973897904369339 545.458306483151 23 66.0226160431507 1 4.44089209850063e-16 1.50546242139171e-13
9 408 Stat3 Gsk3 0.116444761509466 547.331782253666 23 64.1491402726365 1 1.11022302462516e-15 3.76365605347929e-13
10 219 Jak Gsk3 0.0972270586026125 547.331783241571 23 64.1491392847311 1 1.11022302462516e-15 3.76365605347929e-13
11 414 Stat3 Pi3k 0.00323865720911289 550.128339460004 23 61.3525830662981 1 4.77395900588817e-15 1.61837210299609e-12
12 220 Jak Igfr 0.000431831813611869 550.145569905612 23 61.3353526206905 1 4.77395900588817e-15 1.61837210299609e-12
13 225 Jak Pi3k 0.0038696698993625 550.151557166992 23 61.3293653593097 1 4.77395900588817e-15 1.61837210299609e-12
14 409 Stat3 Igfr 0.00217621664460783 550.163245878742 23 61.3176766475602 1 4.88498130835069e-15 1.65600866353088e-12
15 402 Stat3 Akt 0.000884246662417805 550.169105642802 23 61.3118168835005 1 4.88498130835069e-15 1.65600866353088e-12
16 213 Jak Akt 0.000338805400434013 550.202309568355 23 61.2786129579476 1 4.9960036108132e-15 1.69364522406567e-12
17 107 Erk Actr 0.126687899901732 552.877317353801 23 58.6036051725015 1 1.93178806284777e-14 6.54876153305394e-12
18 254 Mek Actr 0.594699695652482 552.880342618551 23 58.6005799077508 1 1.93178806284777e-14 6.54876153305394e-12
19 271 Mek Smad2 0.592686874489201 552.883806503315 23 58.5971160229871 1 1.93178806284777e-14 6.54876153305394e-12
20 124 Erk Smad2 0.126646143317257 552.885235572854 23 58.5956869534483 1 1.93178806284777e-14 6.54876153305394e-12

LA5:Bmp4r -> Smad2

Model residual = 530

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 408 Stat3 Gsk3 0.116449561144749 465.989069170479 24 64.145376955007 1 1.11022302462516e-15 3.75255382323304e-13
2 219 Jak Gsk3 0.097235513336362 465.989071587535 24 64.1453745379512 1 1.11022302462516e-15 3.75255382323304e-13
3 414 Stat3 Pi3k 0.00643045925070463 468.771479804935 24 61.3629663205506 1 4.77395900588817e-15 1.6135981439902e-12
4 409 Stat3 Igfr 0.00181823292543543 468.782367204186 24 61.3520789212998 1 4.77395900588817e-15 1.6135981439902e-12
5 225 Jak Pi3k 0.00389068975889291 468.78885695764 24 61.3455891678462 1 4.77395900588817e-15 1.6135981439902e-12
6 220 Jak Igfr 0.0010206743099913 468.790395318808 24 61.3440508066777 1 4.77395900588817e-15 1.6135981439902e-12
7 402 Stat3 Akt 0.00091623416243391 468.797521827228 24 61.336924298258 1 4.77395900588817e-15 1.6135981439902e-12
8 213 Jak Akt 0.000318413004720444 468.835261333389 24 61.2991847920973 1 4.88498130835069e-15 1.65112368222253e-12
9 415 Stat3 Raf -5.06881620100635 472.226245301838 24 57.9082008236485 1 2.74225087082414e-14 9.26880794338559e-12
10 416 Stat3 Ras -5.03404820081637 472.295028524388 24 57.839417601098 1 2.8421709430404e-14 9.60653778747655e-12
11 412 Stat3 Mek -4.97270293671031 472.418538380271 24 57.7159077452147 1 3.03090885722668e-14 1.02444719374262e-11
12 223 Jak Mek -3.69236068327029 473.280893395087 24 56.8535527303987 1 4.69624339416441e-14 1.58733026722757e-11
13 227 Jak Ras -3.70505238623679 473.298183047908 24 56.8362630775777 1 4.74065231514942e-14 1.6023404825205e-11
14 226 Jak Raf -3.20076089983459 475.091541428191 24 55.0429046972952 1 1.17905685215192e-13 3.98521216027349e-11
15 180 Gsk3 Lifr 0.11965186980617 481.302629649141 24 48.8318164763452 1 2.78876921555593e-12 9.42603994857904e-10
16 179 Gsk3 Jak 0.119652929715791 481.302640242043 24 48.8318058834427 1 2.78876921555593e-12 9.42603994857904e-10
17 8 Activin Fgfr -0.0809971735230671 485.07472186575 24 45.0597242597362 1 1.91116011905024e-11 6.45972120238981e-09
18 29 Actr Fgfr -0.0809971735230671 485.07472186575 24 45.0597242597362 1 1.91116011905024e-11 6.45972120238981e-09
19 386 Smad2 Fgfr -0.0865278085422062 485.075734865781 24 45.0587112597047 1 1.91214821754215e-11 6.46306097529247e-09
20 16 Activin Raf -0.867768169831704 485.333798207924 24 44.8006479175622 1 2.18149942554646e-11 7.37346805834703e-09

LA6:Jak->Gsk3

Model residual = 466

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 180 Gsk3 Lifr 0.254069847636192 417.558306920432 25 48.4307618838654 1 3.42159633959227e-12 1.15307796644259e-09
2 179 Gsk3 Jak 0.254060881262537 417.558306950569 25 48.4307618537283 1 3.42159633959227e-12 1.15307796644259e-09
3 201 Igfr Lifr 0.394663951751604 420.72665430075 25 45.2624145035472 1 1.72324376990218e-11 5.80733150457035e-09
4 200 Igfr Jak 0.394584987718072 420.726654502946 25 45.2624143013512 1 1.72324376990218e-11 5.80733150457035e-09
5 386 Smad2 Fgfr -0.0994390370005753 421.300154420689 25 44.6889143836076 1 2.30960806035796e-11 7.78337916340632e-09
6 29 Actr Fgfr -0.0929468285645529 421.30015446177 25 44.6889143425274 1 2.30960806035796e-11 7.78337916340632e-09
7 8 Activin Fgfr -0.092945417800277 421.300154535314 25 44.6889142689832 1 2.30960806035796e-11 7.78337916340632e-09
8 383 Smad2 Bmp4r -6.6538826951145e-05 421.301339810072 25 44.6877289942248 1 2.31100694136899e-11 7.7880933924135e-09
9 382 Smad2 Bmp4 1 421.301340255647 25 44.6877285486496 1 2.31100694136899e-11 7.7880933924135e-09
10 5 Activin Bmp4r -0.000140131223211644 421.302819512684 25 44.6862492916126 1 2.3127610937479e-11 7.79400488593042e-09
11 26 Actr Bmp4r -0.000140131949540891 421.302819921814 25 44.686248882483 1 2.3127610937479e-11 7.79400488593042e-09
12 4 Activin Bmp4 -0.000140140152534346 421.302822612564 25 44.6862461917328 1 2.3127610937479e-11 7.79400488593042e-09
13 25 Actr Bmp4 -0.000140138869877026 421.30282276421 25 44.686246040087 1 2.3127610937479e-11 7.79400488593042e-09
14 394 Smad2 Raf -0.823998258424749 422.178358169541 25 43.8107106347559 1 3.61719543207073e-11 1.21899486060784e-08
15 391 Smad2 Mek -0.823997051292585 422.178358561652 25 43.8107102426454 1 3.61720653430098e-11 1.21899860205943e-08
16 395 Smad2 Ras -0.823997111449833 422.178358569507 25 43.8107102347903 1 3.61720653430098e-11 1.21899860205943e-08
17 13 Activin Mek -0.766281629474382 422.577980610472 25 43.4110881938253 1 4.43667325100705e-11 1.49515888558938e-08
18 16 Activin Raf -0.766281629474382 422.577980610472 25 43.4110881938253 1 4.43667325100705e-11 1.49515888558938e-08
19 17 Activin Ras -0.766281629474382 422.577980610472 25 43.4110881938253 1 4.43667325100705e-11 1.49515888558938e-08
20 34 Actr Mek -0.766282454667592 422.577980698541 25 43.4110881057558 1 4.43667325100705e-11 1.49515888558938e-08

LA7:Actr->Ras

Model residual = 423

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 179 Gsk3 Jak 0.204451677892591 386.280620930337 26 36.2973595378397 1 1.69393210569524e-09 5.69161187513601e-07
2 180 Gsk3 Lifr 0.204453371104192 386.280621022432 26 36.2973594457445 1 1.69393210569524e-09 5.69161187513601e-07
3 188 Gsk3 Stat3 0.160462852733896 388.7559740907 26 33.8220063774763 1 6.03918492991795e-09 2.02916613645243e-06
4 201 Igfr Lifr 0.329561561344723 390.071887913353 26 32.506092554823 1 1.18819452055163e-08 3.99233358905348e-06
5 200 Igfr Jak 0.329254370188053 390.07188803306 26 32.5060924351164 1 1.18819458716501e-08 3.99233381287443e-06
6 209 Igfr Stat3 0.231284417883316 394.043517175027 26 28.5344632931495 1 9.20454580333185e-08 3.0927273899195e-05
7 276 NoLif Akt 0.0462197611399669 396.116366015608 26 26.4616144525681 1 2.68827253457893e-07 9.0325957161852e-05
8 234 Lifr Akt 0.0462197515000625 396.116366015626 26 26.4616144525501 1 2.68827253457893e-07 9.0325957161852e-05
9 283 NoLif Igfr 0.135739354142486 396.668918586628 26 25.9090618815484 1 3.57885139856684e-07 0.000120249406991846
10 241 Lifr Igfr 0.135735055377168 396.668918601887 26 25.9090618662893 1 3.57885142743264e-07 0.000120249407961737
11 288 NoLif Pi3k 1.28008574350936 396.763764965837 26 25.8142155023389 1 3.75909644634298e-07 0.000126305640597124
12 246 Lifr Pi3k 1.27246998116407 396.763764969147 26 25.8142154990295 1 3.7590964518941e-07 0.000126305640783642
13 282 NoLif Gsk3 0.122375532352744 396.926698188308 26 25.6512822798688 1 4.09023608094472e-07 0.000137431932319743
14 240 Lifr Gsk3 0.122347522718205 396.926698226833 26 25.6512822413432 1 4.090236161991e-07 0.000137431935042898
15 54 Akt Lifr 0.570642649371582 398.054726815378 26 24.5232536527987 1 7.34184103956537e-07 0.000246685858929396
16 432 mTor Lifr 0.469171611541698 398.054726856235 26 24.5232536119416 1 7.34184119610681e-07 0.000246685864189189
17 53 Akt Jak 0.570639127289316 398.054727067896 26 24.5232534002809 1 7.34184200212873e-07 0.000246685891271525
18 431 mTor Jak 0.469129490689945 398.054727139466 26 24.5232533287102 1 7.34184227524359e-07 0.000246685900448185
19 306 Pi3k Lifr 0.0177566337200338 398.054728318739 26 24.5232521494371 1 7.34184676831617e-07 0.000246686051415423
20 305 Pi3k Jak 0.0177204647097351 398.054728546043 26 24.5232519221332 1 7.34184763429013e-07 0.000246686080512148

LA8:Lifr->Akt

Model residual = 396

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 188 Gsk3 Stat3 0.210762379142149 365.592812745445 27 30.5235532324288 1 3.29837653856302e-08 1.10495614041861e-05
2 180 Gsk3 Lifr -0.189581848934756 366.842584662757 27 29.2737813151176 1 6.28402319069465e-08 2.10514776888271e-05
3 179 Gsk3 Jak 0.171841992195559 366.941568501498 27 29.1747974763759 1 6.61338714902371e-08 2.21548469492294e-05
4 209 Igfr Stat3 0.200629565403672 367.740297724291 27 28.3760682535832 1 9.98925683282081e-08 3.34640103899497e-05
5 201 Igfr Lifr -0.203912083852836 368.267519003033 27 27.8488469748407 1 1.3117221664416e-07 4.39426925757936e-05
6 200 Igfr Jak 0.184448518866528 368.327236312088 27 27.789129665786 1 1.35284096591803e-07 4.5320172358254e-05
7 440 mTor Stat3 0.39837963780577 371.434018565152 27 24.6823474127222 1 6.76005264321766e-07 0.000226461763547792
8 62 Akt Stat3 0.480045308095548 371.434018611921 27 24.6823473659528 1 6.76005280642045e-07 0.000226461769015085
9 314 Pi3k Stat3 0.0144374342101018 372.082855177155 27 24.0335108007189 1 9.46735476237137e-07 0.000317156384539441
10 54 Akt Lifr -0.399754419390904 373.124654821559 27 22.991711156315 1 1.62701390082898e-06 0.000545049656777708
11 53 Akt Jak 0.359475065018421 373.124655518437 27 22.9917104594368 1 1.62701449069047e-06 0.000545049854381307
12 431 mTor Jak 0.298026670226817 373.124655630479 27 22.9917103473955 1 1.62701458550352e-06 0.000545049886143679
13 305 Pi3k Jak 0.0110225808628161 373.12465583613 27 22.9917101417441 1 1.62701475947546e-06 0.000545049944424279
14 432 mTor Lifr 1 373.124656256152 27 22.9917097217218 1 1.62701511496888e-06 0.000545050063514575
15 404 Stat3 Bmp4r 5.06415768645462 374.205542728137 27 21.9108232497375 1 2.85618475537319e-06 0.000956821893050019
16 214 Jak Bmp4 1 374.205542820453 27 21.9108231574212 1 2.8561848928188e-06 0.000956821939094298
17 215 Jak Bmp4r 6.32096456749799 374.205542821838 27 21.9108231560358 1 2.85618489492823e-06 0.000956821939800957
18 403 Stat3 Bmp4 1 374.205546222778 27 21.910819755096 1 2.85618995665704e-06 0.000956823635480108
19 229 Jak Smad2 0.161494499103621 377.074644716044 27 19.0417212618297 1 1.27891401775493e-05 0.00428436195947902
20 418 Stat3 Smad2 0.123492270761975 377.074644787337 27 19.0417211905368 1 1.27891406553893e-05 0.00428436211955542

LA9:Gsk3->Lifr

Model residual = 367

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 404 Stat3 Bmp4r 50.6769951795926 344.033027503324 28 22.8095573197015 1 1.78873964251647e-06 0.000597439040600501
2 215 Jak Bmp4r 5.85640802886813 344.033027595869 28 22.8095572271561 1 1.78873972866977e-06 0.000597439069375703
3 214 Jak Bmp4 1 344.033032218802 28 22.809552604224 1 1.78874403133911e-06 0.000597440506467263
4 403 Stat3 Bmp4 1 344.033033501447 28 22.8095513215787 1 1.78874522516193e-06 0.000597440905204085
5 229 Jak Smad2 0.147929314286488 347.417696566259 28 19.4248882567668 1 1.04634570883277e-05 0.00349479466750145
6 418 Stat3 Smad2 0.123181188567727 347.417699989782 28 19.4248848332438 1 1.04634758444355e-05 0.00349480093204146
7 212 Jak Actr 1 347.495188072543 28 19.3473967504826 1 1.08967696662576e-05 0.00363952106853004
8 401 Stat3 Actr 1 347.495188197578 28 19.3473966254471 1 1.0896770379798e-05 0.00363952130685253
9 236 Lifr Bmp4r -69.2199856317919 349.285169674623 28 17.5574151484025 1 2.78761586077758e-05 0.00931063697499712
10 235 Lifr Bmp4 1 349.285173499709 28 17.5574113233167 1 2.78762146838085e-05 0.00931065570439204
11 281 NoLif Fgfr -0.0965806936461771 350.878888792454 28 15.963696030572 1 6.45689150552409e-05 0.0215660176284505
12 290 NoLif Ras -0.93028535245474 351.286180278895 28 15.5564045441308 1 8.0079907832431e-05 0.026746689216032
13 289 NoLif Raf -0.930287727289117 351.28618031167 28 15.5564045113559 1 8.00799092206539e-05 0.0267466896796984
14 286 NoLif Mek -0.93028737169618 351.286180311851 28 15.5564045111748 1 8.00799092283144e-05 0.026746689682257
15 152 Fgfr Bmp4r 20.3166065973017 351.776763850773 28 15.0658209722526 1 0.000103826322989442 0.0346779918784736
16 151 Fgfr Bmp4 1 351.776771612457 28 15.0658132105688 1 0.00010382674993159 0.0346781344771511
17 170 Gsk3 Actr 1 351.826168502886 28 15.01641632014 1 0.000106580000543754 0.0355977201816138
18 191 Igfr Actr 1 352.326159499371 28 14.5164253236542 1 0.000138942796143127 0.0464068939118044
19 220 Jak Igfr 0.464138874014621 352.670882304326 28 14.1717025186995 1 0.000166861181154943 0.055731634505751
20 409 Stat3 Igfr 0.415523726337933 352.670882508435 28 14.1717023145901 1 0.000166861199256463 0.0557316405516586

LA10:Jak->Bmp4r

Model residual = 344

Link Extension :
adj_idx from to value residual df Res_delta df_delta pval adj_pval
1 281 NoLif Fgfr -0.102330296068047 326.947159717004 29 17.0858676194478 1 3.57271760821343e-05 0.0118971496353507
2 286 NoLif Mek -0.95499403504574 327.383962044685 29 16.6490652917671 1 4.49724642367366e-05 0.0149758305908333
3 290 NoLif Ras -0.954993006354123 327.383962071378 29 16.6490652650744 1 4.49724648695637e-05 0.0149758308015647
4 289 NoLif Raf -0.95499328934535 327.383962124094 29 16.6490652123577 1 4.49724661194528e-05 0.0149758312177778
5 136 Fgf4 Igfr -0.188380198883811 329.884330788765 29 14.1486965476873 1 0.00016891409373454 0.0562483932136018
6 141 Fgf4 Pi3k -1.83482605059102 330.049582154548 29 13.9834451819045 1 0.000184427358768002 0.0614143104697447
7 54 Akt Lifr 2.62319646965679 330.089387571776 29 13.9436397646759 1 0.000188373912535678 0.0627285128743808
8 53 Akt Jak -1.67773793168286 330.089388118165 29 13.9436392182866 1 0.00018837396728788 0.062728531106864
9 431 mTor Jak -1.39227059690346 330.089388353278 29 13.9436389831743 1 0.000188373990847812 0.0627285389523214
10 305 Pi3k Jak -0.075439777699395 330.089388426539 29 13.9436389099135 1 0.000188373998189051 0.062728541396954
11 306 Pi3k Lifr 1 330.089389731358 29 13.9436376050941 1 0.000188374128941571 0.0627285849375431
12 432 mTor Lifr 1 330.089390244238 29 13.9436370922141 1 0.000188374180335904 0.062728602051856
13 409 Stat3 Igfr 0.41869121884932 330.180081070318 29 13.8529462661345 1 0.000197686548991216 0.0658296208140749
14 220 Jak Igfr 0.476759506832458 330.180081204178 29 13.8529461322745 1 0.000197686563073063 0.06582962550333
15 405 Stat3 Erk 0.521783221868987 330.267551034026 29 13.7654763024265 1 0.000207107453763733 0.0689667821033231
16 216 Jak Erk 0.555417749315504 330.267551046827 29 13.7654762896253 1 0.000207107455175048 0.068966782573291
17 135 Fgf4 Gsk3 -0.11036008200672 330.296405830492 29 13.73662150596 1 0.000210313444124255 0.0700343768933769
18 239 Lifr Fgfr -0.100025968227278 331.03222515939 29 13.0008021770625 1 0.000311357562982395 0.103682068473138
19 225 Jak Pi3k 4.54623075626334 331.054906372612 29 12.9781209638404 1 0.000315152090948345 0.104945646285799
20 414 Stat3 Pi3k 3.82780031506277 331.054906420842 29 12.9781209156102 1 0.000315152099066518 0.10494564898915

Summary

Links Added and Residuals

Model_iteration Links res_p_005_XX res_p_005_XO
1 Init Init Network 2056.3 1603.72
2 1 Jak->Fgfr 1515 1063.56
3 2 Gsk3->Igfr 971.09 970.63
4 3 Erk->Raf 932.31 720.06
5 4 Bmp4r->Fgfr 798.33 611.48
6 5 Bmp4r->Smad2 752.29 530.13
7 6 Jak->Gsk3 691.89 465.99
8 7 Actr->Ras 645.07 422.58
9 8 Lifr->Akt 622.06 396.12
10 9 Gsk3->Lifr 602.97 366.84
11 10 Jak->Bmp4r 572.24 344.03